Fishery energy-saving and environmental protection play an important role in promoting the development of marine economy. Compared with traditional marine power system, hybrid propulsion system has some advantages, such as, wide speed range, strong driving force, easy positive inversion, small volume, flexible layout, convenient installation and maintenance, low vibration and noise. When tuna longliner is working, the main engine is in the low speed and low load operation conditions. It will cause higher specific fuel consumption and carbon deposition. Then the back pressure of turbocharger will increase, and the surge will be caused in the end. In addition, the main engine is limited by minimum stable engine speed. Suddenly quick and slow speed is not conducive to the production. According to the methods and characteristics of tuna longliner, a kind of electromechanical hybrid propulsion system is presented in this paper. Sectional drive parallel electrical hybrid propulsion structure is used in this system. It can reduce the dependence on main engine when tuna longliner sails or works. The redundancy of propulsion system can be improved, as well as the operating flexibility. The ship maneuverability and integrated propulsion efficiency can be promoted significantly. Through the analysis of the economic and environmental protection index, compared with the conventional hybrid tuna longliner, the general fuel consumption can reduce by 20% under the same condition in shooting, cruising and reeling. Also the system reliability, safety and comprehensive propulsion efficiency are improved.